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Physiol. Genomics 4: 13-24, 2000;
1094-8341/00 $5.00
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Received 26 April 2000; accepted in final form 18 August 2000.
Physiological Genomics 4:13-24 (2000)
1094-8341/00 $5.00 © 2000 American Physiological Society

A set of canine interrepeat sequence PCR markers for high-throughput genotyping

MANJULA DAS1, HAKAN SAKUL2, JULIUS KONG1, GREGORY M. ACLAND3 and JERRY PELLETIER1,4

1 Department of Biochemistry
4 Department of Oncology, McGill University, Montreal, Quebec, Canada H3G 1Y6
2 Department of Statistical Genetics, Parke Davis Laboratory for Molecular Genetics, Alameda, California 94502
3 James A. Baker Institute for Animal Health, New York State College of Veterinary Medicine, Cornell University, Ithaca, New York 14853-6401

One hundred and sixteen interspersed repetitive DNA sequence (IRS)-PCR markers have been developed and characterized from Canis familiaris for high-throughput filter-based genotyping. We present a detailed analysis of markers produced by amplification using primers directed to the conserved regions of the C. familiaris short interspersed nuclear element (Can-SINE). The majority of IRS-PCR markers developed were moderately to highly polymorphic with mean heterozygosity (HET) and polymorphism information content (PIC) values of ~0.6. The HET value for 22.3% of the markers exceeded 0.7. We also demonstrate that sequence variation of Can-SINEs between breeds is significant and also represents a rich source of polymorphisms. Mapping of 73 of the markers to the existing integrated linkage-radiation hybrid map enriches the map as well as establishes the utility of the markers. The significance and utility of this new class of IRS-PCR Can-SINE-based markers for high-throughput genotyping is discussed. This method can also be extended to other species that are currently map-poor but have a sufficiently high density of SINEs to allow IRS-PCR.

IRS-PCR markers; Canis familiaris; genotyping; polymorphism; radiation hybrid mapping; polymerase chain reaction; interspersed repetitive DNA sequence




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